Genomic polymorphism of Trifolium repens root nodule symbionts from heavy metal-abundant 100-year-old waste heap in southern Poland

Abstract

In total, 77 rhizobial strains isolated from the root nodules of T. repens, inhabiting heavy metal-contaminated waste heap (36 isolates) and control grassland (41 ones) in southern Poland, were analyzed for genome polymorphism and strength of the heavy metals’ (mainly Zn, Pb, Cd) selective pressure on bacterial genome polymorphism using two PCR-based techniques, ERIC- (enterobacterial repetitive intergenic consensus) and REP-PCR (repetitive extragenic palindromic) sequences. Both methods of different discriminatory power index (D) (ERIC-PCR D = 0.9737; REP-PCR D = 0.9826) allowed to distinguish 47 and 44 rhizobial strains, respectively. Combined analysis of ERIC-PCR and REP-PCR DNA amplicons differentiated all tested isolates. Both ERIC- and REP-PCR DNA fingerprinting techniques showed significant decline of the genome polymorphism (h) in rhizobial population from metalliferous waste heap (h = 0.89 ± 0.03; h = 0.90 ± 0.02, respectively) compared to rhizobia from control non-metalliferous area (h = 0.99 ± 0.01; h = 0.98 ± 0.02, respectively) as well as substantial differences in the genomic polymorphism between both these populations (FST = 0.162, p = 0.008; FST = 0.170, p = 0.000, respectively).Electronic supplementary materialThe online version of this article (10.1007/s00203-019-01708-x) contains supplementary material, which is available to authorized users.

Trifolium repens-Associated Bacteria as a Potential Tool to Facilitate Phytostabilization of Zinc and Lead Polluted Waste Heaps

“…Their dissimilar presence in plant tissues might be due to differences in access to nutrients or specific traits of the host plant [ 58 ]. Moreover, it was shown that apart from rhizobia, which are permanent inhabitants of white clover root nodules [ 15 , 22 , 23 ], nodules are also inhabited by many other non-rhizobial bacterial taxa, e.g., Bacillus sp., Pseudomonas sp., Stenotrophomonas maltophilia , Micrococcus luteus , Erwinia persicina , and Chryseobacterium lathyri ( Figure 3 B). Muresu et al [ 59 ] demonstrated that nodules of the legume plant Hedysarum sp.…”

“…In order to determine the relative taxonomic biodiversity of studied microbial communities originating from the three metal polluted sites and the non-polluted reference site, the Shannon’s diversity index ( H’ ) was used [ 23 , 35 , 36 ]. For the evaluation of the significance of the differences in taxonomical richness between studied microbial communities, their Shannon’s diversity index ( H’ ) values were subjected to the non-parametric U Mann–Whitney statistical test at the significance level p < 0.05 with the usage of Statistica 13 software.…”

“…Legumes include several pioneer species, able to colonize marginal soils and to improve the nutritional status and organic matter content (and thus water-holding capacity) of the soils they are growing on. Trifolium repens (white clover) is such a species that spontaneously colonizes most Zn–Pb containing waste heaps in southern Poland [ 22 , 23 ].…”

“…Oleńska and Małek [ 23 ] have recently demonstrated that the high metal concentrations in the soils of these waste heaps act as a natural selection factor shaping the genetic structure of native bacterial populations. A reduction of the genomic polymorphism of Rhizobium leguminosarum bv.…”

Comparative Assessment of Different PCR-Based Typing Methods of Pseudomonas aeruginosa Isolates

“…To determine the index of strain diversity (ISD), that measured as the frequency of diverse genotypes, the following equation was used. 30 ISD % ð Þ¼ 100% number of geno types=total number of isolates ð Þ…”